1 data prep spatial layers

read in some data A and data B. Modify some things, and save as layer 1.

2 data prep other layers

This sources a script that modifies another new layer (tableC) and saves it as table2 and table3, external to the direct Rmd path. It also sources a separate script that reads a previously-saved layer (table 1) and gapfills, saving as table1a.

3 model

sourced script reads in layers 1a, 2, and 3, and does some stuff, and saves the results as layers D and E.

4 The next section (below the divider) is the footer, knitted as a child

The code for the R code chunk header looks like this:

{r child = file.path(dir_git, 'src/templates/ohibc_prov_ftr.Rmd')}

Note that it is executed as if it were just part of this main document; it numbers the section (“Provenance”) as a continuation of the numbering, and the variables are evaluated in the environment of the main document.

5 Provenance

Run ID: 18 (a9b5183); run tag: “standard run”
Run elapsed time: 4.619 seconds; run memory usage: NA MB
System info: System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.
Session info
- R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).
- Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base
- Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3

##   run_id      run_tag                 run_date
## 1     18 standard run Thu May  5 12:23:50 2016
## 2     18 standard run Thu May  5 12:23:50 2016
## 3     18 standard run Thu May  5 12:23:50 2016
## 4     18 standard run Thu May  5 12:23:50 2016
## 5     18 standard run Thu May  5 12:23:50 2016
## 6     18 standard run Thu May  5 12:23:50 2016
##                                          parent_fn
## 1 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd
## 2 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd
## 3 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd
## 4 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd
## 5  ~/github/ohibc/rmd_testing/1_data_prep_sample.R
## 6  ~/github/ohibc/rmd_testing/1_data_prep_sample.R
##                                 file_loc filetype
## 1  ~/github/ohibc/rmd_testing/tableA.csv    input
## 2 ~/github/ohibc/rmd_testing/tableA1.csv    input
## 3  ~/github/ohibc/rmd_testing/tableB.csv    input
## 4  ~/github/ohibc/rmd_testing/table1.csv   output
## 5  ~/github/ohibc/rmd_testing/tableC.csv    input
## 6  ~/github/ohibc/rmd_testing/table3.csv   output
##                                                                                              commit_url
## 1                  https://github.com/OHI-Science/ohibc/commit/8b48c047ef11e01d13c8b61e83e8edc6cce99cf9
## 2                                                                         no version control info found
## 3                  https://github.com/OHI-Science/ohibc/commit/00b6e10615d39b60a92958f7d8887c9e1091af54
## 4 Previous commit: https://github.com/OHI-Science/ohibc/commit/893b6768bfa73aae999c60b5c61cdfd2e501944e
## 5                  https://github.com/OHI-Science/ohibc/commit/00b6e10615d39b60a92958f7d8887c9e1091af54
## 6 Previous commit: https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb
##                         commit_author                      commit_date
## 1 Casey O'Hara <ohara@nceas.ucsb.edu>   Sat Apr 30 12:01:16 2016 -0700
## 2                                <NA>                             <NA>
## 3 Casey O'Hara <ohara@nceas.ucsb.edu>   Sat Apr 30 10:25:32 2016 -0700
## 4 Casey O'Hara <ohara@nceas.ucsb.edu>   Fri Nov 13 11:03:56 2015 -0800
## 5 Casey O'Hara <ohara@nceas.ucsb.edu>   Sat Apr 30 10:25:32 2016 -0700
## 6 Casey O'Hara <ohara@nceas.ucsb.edu>    Tue May 3 16:14:15 2016 -0700
##   uncommitted_changes elapsed_time memory_use
## 1               FALSE        4.619         NA
## 2                TRUE        4.619         NA
## 3               FALSE        4.619         NA
## 4               FALSE        4.619         NA
## 5               FALSE        4.619         NA
## 6               FALSE        4.619         NA
##                                                              sys_info
## 1 System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.
## 2 System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.
## 3 System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.
## 4 System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.
## 5 System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.
## 6 System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.
##                                                                                                                ses_info
## 1 R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).
## 2 R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).
## 3 R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).
## 4 R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).
## 5 R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).
## 6 R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).
##                                                                            base_pkgs
## 1 Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base
## 2 Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base
## 3 Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base
## 4 Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base
## 5 Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base
## 6 Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base
##                                                      attached_pkgs
## 1 Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3
## 2 Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3
## 3 Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3
## 4 Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3
## 5 Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3
## 6 Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3
##                                        rdf_subject
## 1            ~/github/ohibc/rmd_testing/tableA.csv
## 2           ~/github/ohibc/rmd_testing/tableA1.csv
## 3            ~/github/ohibc/rmd_testing/tableB.csv
## 4 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd
## 5            ~/github/ohibc/rmd_testing/tableC.csv
## 6  ~/github/ohibc/rmd_testing/1_data_prep_sample.R
##                                         rdf_object       rdf_predicate
## 1 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd           prov:used
## 2 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd           prov:used
## 3 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd           prov:used
## 4            ~/github/ohibc/rmd_testing/table1.csv prov:wasGeneratedBy
## 5  ~/github/ohibc/rmd_testing/1_data_prep_sample.R           prov:used
## 6            ~/github/ohibc/rmd_testing/table3.csv prov:wasGeneratedBy
##                                   run_hash
## 1 a9b5183ef53f0bb3b71c0e86c1b93617d0748c20
## 2 a9b5183ef53f0bb3b71c0e86c1b93617d0748c20
## 3 a9b5183ef53f0bb3b71c0e86c1b93617d0748c20
## 4 a9b5183ef53f0bb3b71c0e86c1b93617d0748c20
## 5 a9b5183ef53f0bb3b71c0e86c1b93617d0748c20
## 6 a9b5183ef53f0bb3b71c0e86c1b93617d0748c20

Provenance summary for run 18 (a9b5183): standard run (Thu May 5 12:23:50 2016)
file_name	file_dir	filetype	uncomm_chgs	commit_hash
table1.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	893b676
table1a.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	a7e123b
table2.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	a7e123b
table3.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	a7e123b
tableA.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	8b48c04
tableA1.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	TRUE	NA
tableB.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	00b6e10
tableC.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	00b6e10
table1.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	893b676
table1a.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
table2.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
table3.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
tableD.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
tableE.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
0_sample_script.Rmd	/Users/caseyohara/github/ohibc/rmd_testing/.	parent_script	TRUE	d569b5a
1_data_prep_sample.R	/Users/caseyohara/github/ohibc/rmd_testing	sourced_script	TRUE	725220e
1a_gapfill.R	/Users/caseyohara/github/ohibc/rmd_testing	sourced_script	FALSE	725220e
2_model_sample.R	/Users/caseyohara/github/ohibc/rmd_testing	sourced_script	FALSE	725220e

R Markdown test rmd

Compiled on Thu May 5 12:23:44 2016 by caseyohara

1 data prep spatial layers

2 data prep other layers

3 model

4 The next section (below the divider) is the footer, knitted as a child

5 Provenance